| GeneMark | |
| A family of gene prediction programs developed at Georgia Institute of Technology , Atlanta, Georgia, USA. |
| What's New: Pre-print GeneMark-ETP |
Supported by NIH  |
| Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes | |
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Novel prokaryotic genomic sequences can be analyzed by the self-training software tool GeneMarkS-2 (sequences longer than 50 Kb). For some species pre-trained model parameters are ready and available through the GeneMark.hmm. Metagenomic sequences and individual short sequences (sequences < 50 kb) can be analyzed by MetaGeneMark. |
| Gene Prediction in Eukaryotes | |
| Novel eukaryotic genomes can be analyzed by the self-training GeneMark-ES. The fungal mode of GeneMark-ES accounts for fungal-specific intron organization. GeneMark-ET integrates into GeneMark-ES information on mapped RNA-Seq reads. GeneMark-EP+ integrates into GeneMark-ES information on cross-species protein sequences. GeneMark-ETP integrates into GeneMark-ES both types of external information, RNA reads and cross-species proteins. |
| Gene Prediction in Transcripts | |
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Sets of eukaryotic transcripts can be analyzed by GeneMarkS-T. |
| Gene Prediction in Viruses, Phages and Plasmids | |
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Sequences of viruses, phages or plasmids can be analyzed either by GeneMarkS (sequences > 50 Kb) or MetaGeneMark (sequences < 50 kb) |
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All the software tools mentioned here are available for download. The GeneMark software is a part of genome annotation pipelines at NIH NCBI (for prokaryotes) and DOE JGI (for eukaryotes) as well as others: |
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Eukaryotic genome annotation pipelines:
For more information see Background and Publications. |
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Borodovsky Group Group news Gene Prediction Programs
International Conferences Bioinformatics Studies at Georgia Tech |